From what you've described, I'd be inclined to believe that signatures did not exist for this file at the time it was created, which would be why Auto-Protect failed to pick it up. While it's true that the Scheduled Scan's Insight lookup (reputation based scan) might have detected the file, this is by no means guaranteed.
If current attempts to access the file cause Auto-Protect to remove it, then it certainly suggests sigs have been developed and released after the initial "drop".
There's no real way of "dropping" a file without Auto-Protect seeing it (short of booting a machine to an alternative OS that is not running any AV, and using that to write the file). And even then, once booted back into Windows, the file would get caught on-access (once again, assuming sigs exist).
At this point, I'd probably suggest you schedule more regular full scans.
With regards to your manual scan failing to find the offending file, perhaps the below article would help:
http://www.symantec.com/docs/TECH103126
http://www.symantec.com/docs/TECH99222